Don't quote me on this ( you may need to check it out for yourself ) but when doing lots of reseach, on anti virus, I read that Malwarebytes don't scan for rootkits.......this was because it is a very deep and thorough scan ( delving into the bowels of a computer ) and therefore causing potential slowing and problems with the computer's operations; while the scan is taking place.  Whereas the scan had been achieved / perfected by AVG.......Malwarebytes had not yet done so and therefore didn't incorporate that particular scan into it's scanning package. It has the option to tick the box ( as shown in your pic. ) because they hope to be able to do it in the future, but right now; ticking it will not mean it will be carried out.  On AVG, it is possible to scan for rootkits ONLY and I did this operation, only yesterday, while altering my scanning schedules.  If it's possible to run the same operation on Malwarebytes, it would give you a definitive answer; as to whether they now do it or not.